run("Action Bar","/plugins/ActionBar/_ActionbarSA.txt");
call("ij.Prefs.set", "pre.cont_sat", 0.35);
call("ij.Prefs.set", "pre.ball_rad", 20);
call("ij.Prefs.set", "pre.thresh_rad", 10);
call("ij.Prefs.set", "pre.thresh_bias", -100);
call("ij.Prefs.set", "pre.min_obj", 50);
call("ij.Prefs.set", "pre.max_obj", 7000000);
exit();

<line>
<button>
label=Options
icon=noicon
arg=<macro>
	run("Action Bar","/plugins/ActionBar/_ActionbarOptions.txt");
</macro>
</button>


<button>
label=Toggle Machine-marked objects
icon=noicon
arg=<macro>
	ojShowImage(1);
	tog = call("ij.Prefs.get", "pre.qual_tog", "this is wrong");
	lis = call("ij.Prefs.get", "pre.val0", "this is wrong");
	for(i = ojFirstObject(1); i <= ojLastObject(1); i ++){
		ojSelectObject(i);
		obId = ojIndexToId(i);
	if(tog==false){
		ojQualify(i, true);
	}else if(tog==true && lis.contains(toString(obId))){
		ojQualify(i, false);
	}
}
if(tog==false){
		call("ij.Prefs.set", "pre.qual_tog", true); //these are for the next time the macro is called
}else if(tog==true){
		call("ij.Prefs.set", "pre.qual_tog", false);
}

</macro>
</button>


<button>
label=select Marker and ROI
icon=noicon
arg=<macro>
	n = obj_num = getNumber("enter object number: ", 1);
	run("3D Manager");
	nb_obj = 0;
	Ext.Manager3D_Count(nb_obj);
	if (nb_obj==0){
		showMessage("There are no regions in the 3d ROI manager");
	}else{
		run("3D Manager");
		Ext.Manager3D_DeselectAll()
		Ext.Manager3D_MultiSelect();
		for(i = 0; i < nb_obj; i ++){
			name = "";
			Ext.Manager3D_GetName(i, name);
			name = split(name, "-");
			if(name[0].contains(n)){
				Ext.Manager3D_Select(i);
			}
		}
		Ext.Manager3D_MonoSelect();
	}
	ojSelectObject(n); 
	ojShowObject(n);
</macro>
</button>



<button>
label=Update ObjJ markers
icon=noicon
arg=<macro>
	showMessage("Select location of object marker lists");
	path = getDir("Location of object marker lists");
	image_num = getNumber("image number:", 1);
	ojShowImage(image_num);

	numRows = getValue("results.count");
	IJ.deleteRows(0,numRows);

	if(is("composite")){
	}else{
		row = 0;
		start = ojFirstObject(image_num);
		end = ojLastObject(image_num);
		for (i = start; i <= end; i++, row++) {
			ojSelectObject(i);
			name = ojGetItemName();
			x = ojXPos(1);
			y = ojYPos(1); 
			z = ojZPos(1);
			setResult("X", row, x);
			setResult("Y", row, y);
			setResult("Z", row, z);
		}
		saveAs("Results", path+"chan1_model.csv");
	}
	showMessage("new lists saved in project folder");
	run("Close");
</macro>
</button>


</line>

<line>
<button>
label=Run Simple Neurite Tracer
icon=noicon
arg=<macro>
	cellfill = getNumber("enter channel number of cell fill", 1);
	ojShowImage(1);
	run("Duplicate...", "duplicate channels="+cellfill);
	run("Simple Neurite Tracer");
</macro>
</button>

<button>
label=Delete objects in image
icon=noicon
arg=<macro>
	image_num = getNumber("image number: ", 1);
	ojShowImage(image_num);
	while(ojLastObject(image_num)-ojFirstObject(image_num)>=0){
		n = ojFirstObject(image_num);
		ojDeleteObject(n);
	} 
</macro>
</button>

<button>
label=Identify objects in first image
icon=noicon
arg=<macro>
	ojSetComposite(false);
	if(ojNObjects()==0){
		doCommand("MarkerGuesser"); 	//run("MarkerGuesser"); does not work for some reason
	}else if(ojNObjects()>0){
		redo = getBoolean("There are already objects marked. Redo and delete all objects in all images?");
		if(redo == true){
			ojDeleteAllObjects();
			doCommand("MarkerGuesser");
		}
	}
	
</macro>
</button>

<button>
label=Measure Intensity
icon=noicon
arg=<macro>
	ojShowImage(1);
	marker_channel = getNumber("channel to use to ROI: ", 1);
	obj_size = getNumber("radius of objs: ", 15);

	num_objs = ojNObjects();
	height = ojGetImageValue(1, "height") ;
	width = ojGetImageValue(1, "width") ;
	stacksize = ojGetImageValue(1, "stacksize") ;

	name = ojGetImageName(1);
	name = replace(name, ".tif", "");


	ojShowImage(1);
	run("Duplicate...", "duplicate channels="+marker_channel+"");
	rename("duplicate1");
	run("8-bit");

	for(n = 1; n <= num_objs; n ++){
		ojSelectObject(n);
		ojName = ojGetItemName();
	

		x = ojXPos(1);
		y = ojYPos(1); 
		z = ojZPos(1);
	
	
		if(z%3==marker_channel || (z%3)+3==marker_channel){
			stack_z = ((z/3));
			run("3D Draw Shape", "size="+width+","+height+","+(stacksize/3)+" center="+x+","+y+","+stack_z+" radius="+obj_size+","+obj_size+","+obj_size+" vector1=1.0,0.0,0.0 vector2=0.0,1.0,0.0 res_xy=1.000 res_z=1.000 unit=pixels value=255");
			run("3D Intensity Measure", "objects=Shape3D signal=duplicate1");
			selectWindow("Shape3D");
			run("3D Manager");
			Ext.Manager3D_AddImage();
			selectWindow("duplicate1");
			close("\\Others");
		
		}
	}
	

	selectWindow("Results");
</macro>
</button>



<button>
label=Mask entire cell
icon=noicon
arg=<macro>
	showMessage("open branch files");
	open();
	name_branches = getTitle();
	xy_dilate = getNumber("XY-dilation", 20);z_dilate = getNumber("z-dilation", 10);
	run("8-bit");
	run("8-bit");
	for(i = 0; i < xy_dilate-z_dilate; i ++){
		run("Dilate", "stack");
	}
	for(i = 0; i < z_dilate; i ++){
		run("Dilate (3D)");
	}



	ojShowImage(1);
	run("Duplicate...", "duplicate");
	run("Split Channels");
	blue = getImageID();

	name = newArray(3);

	for(i = 0; i < 3; i ++){
		id = blue+i;
		selectImage(id);
		run("8-bit");
		run("Subtract...", "value=50 stack");
		name[i] = getTitle();
		imageCalculator("Min create 32-bit stack", name_branches, name[i]);
		rename("maskedResult_"+i);
	}
	run("Merge Channels...", "c1=maskedResult_0 c2=maskedResult_1 c3=maskedResult_2 create");

	for(i = 0; i < 3; i ++){
		id = blue+i;
		selectImage(id);
		setOption("Changes", false);
		close();
	}
</macro>
</button>
</line>